Individual sample stayed at 'Finding clipped reads'

[YaliHao]

Hi, Chrisjrt!
I have run the test files correctly. However, when I used hafeZ to run 40 data in batches with 4 threads, it stayed at one sample for 6 hours while making no progress(it didn't stop, and there was no error messages). I checked the sample was GCA_003573835.1(DRR160049). Then I ran the sample alone using the code(in case 4 threads lead to the results, I used 64 threads this time ):

hafeZ.py -f /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fna/fna/genbank/bacteria/GCA_003573835.1/GCA_003573835.1_ASM357383v1_genomic.fna -r1 /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fastq/Staphylococcus_aureu/DRR160049/DRR160049_1.fastq -r2 /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fastq/Staphylococcus_aureu/DRR160049/DRR160049_2.fastq -o GCA_003573835.1 -D /dssg/home/acct-clsjhh/clsjhh/hyl/software/hafeZ/hafeZ_db -T phrogs -t 64

and the log.out showed

[M::mm_idx_gen::0.063*1.06] collected minimizers
[M::mm_idx_gen::0.076*5.15] sorted minimizers
[M::main::0.076*5.15] loaded/built the index for 2 target sequence(s)
[M::mm_mapopt_update::0.076*5.15] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 2
[M::mm_idx_stat::0.082*4.85] distinct minimizers: 471983 (99.02% are singletons); average occurrences: 1.020; average spacing: 5.994; total length: 2885609
[M::worker_pipeline::2.239*12.31] mapped 180580 sequences
[M::worker_pipeline::2.640*15.04] mapped 180630 sequences
[M::worker_pipeline::3.004*16.56] mapped 180878 sequences
[M::worker_pipeline::3.397*17.63] mapped 180928 sequences
[M::worker_pipeline::4.030*17.36] mapped 180836 sequences
[M::worker_pipeline::4.551*17.63] mapped 180910 sequences
[M::worker_pipeline::4.976*18.13] mapped 181050 sequences
[M::worker_pipeline::5.423*18.50] mapped 181212 sequences
[M::worker_pipeline::5.898*18.73] mapped 181028 sequences
[M::worker_pipeline::6.325*19.12] mapped 181200 sequences
[M::worker_pipeline::6.825*19.16] mapped 181404 sequences
[M::worker_pipeline::7.296*19.30] mapped 181418 sequences
[M::worker_pipeline::7.772*19.40] mapped 179944 sequences
[M::worker_pipeline::8.215*19.55] mapped 179966 sequences
[M::worker_pipeline::8.650*19.73] mapped 180182 sequences
[M::worker_pipeline::9.574*18.85] mapped 180244 sequences
[M::worker_pipeline::10.047*18.94] mapped 180366 sequences
[M::worker_pipeline::10.546*18.98] mapped 180312 sequences
[M::worker_pipeline::11.038*19.03] mapped 180376 sequences
[M::worker_pipeline::11.560*19.02] mapped 180266 sequences
[M::worker_pipeline::12.011*19.12] mapped 180410 sequences
[M::worker_pipeline::12.369*18.83] mapped 180652 sequences
[M::worker_pipeline::12.701*18.37] mapped 180446 sequences
[M::worker_pipeline::12.812*18.22] mapped 53438 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -ax sr -t 64 -o /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_hafez/GCA_003573835.1/temp_minimap.sam /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_hafez/GCA_003573835.1/temp_genome.fasta /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fastq/Staphylococcus_aureu/DRR160049/DRR160049_1.fastq /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fastq/Staphylococcus_aureu/DRR160049/DRR160049_2.fastq
[M::main] Real time: 12.837 sec; CPU: 233.411 sec; Peak RSS: 0.696 GB
[bam_sort_core] merging from 0 files and 64 in-memory blocks...

Running hafeZ version 1.0.4 with the following settings:
hafeZ.py -f /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fna/fna/genbank/bacteria/GCA_003573835.1/GCA_003573835.1_ASM357383v1_genomic.fna -r1 /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fastq/Staphylococcus_aureu/DRR160049/DRR160049_1.fastq -r2 /dssg/home/acct-clsjhh/clsjhh/hyl/SPI/test_provirus_del/ESKAPE/ESKAPE_fastq/Staphylococcus_aureu/DRR160049/DRR160049_2.fastq -o GCA_003573835.1 -D /dssg/home/acct-clsjhh/clsjhh/hyl/software/hafeZ/hafeZ_db -c 3.5 -b 3001 -w 4000 -m 6 -t 64 -p 0.1 -z 3.5

##################################################
################# Running hafeZ ##################
##################################################

################ Processing fasta ################
############### Done: 0.96 seconds ###############

########### Calculating genome length ############
############# Done: 0.00000 seconds ##############

########### Mapping reads to assembly ############
############## Done: 12.94 seconds ###############

############## Generating BAM file ###############
Running samtools
finished running samtools
############## Done: 35.61 seconds ###############

########### Generating coverage depths ###########
Running mosdepth
finished running mosdepth
############### Done: 6.92 seconds ###############

################ Smoothing signal ################
############### Done: 8.38 seconds ###############

################ Getting Z-scores ################
############### Done: 0.63 seconds ###############

##### Finding potential regions of interest ######
############### Done: 0.01 seconds ###############

####### Merging close regions of interest ########
############### Done: 0.16 seconds ###############

####### Removing small regions of interest #######
############## Done: 0.0002 seconds ##############

######## Parsing and processing sam file #########
############### Done: 2.89 seconds ###############

####### Checking for rois near contig ends #######
############### Done: 0.00 seconds ###############

############# Finding clipped reads ##############

and it remained this state for nearly two hours. The corresponding directory contains the file

The same situation appeared on the GCA_019042295.1(SRR14879700)
Would you please give me some suggestions?
Thank you!